void scanArrived_Response(object sender, MsScanEventArgs e)
{
try
{
Console.WriteLine("Scan arrived.");
logfile.WriteLine("Scan arrived.");
if (!authorized_for_run)
{
Console.WriteLine("Ignoring pre-emptive scan.");
logfile.WriteLine("Ignoring pre-emptive scan.");
return;
}
else if (!accepting_scans)
{
Console.WriteLine("Ignoring wait-time scan.");
logfile.WriteLine("Ignoring wait-time scan.");
return;
}
IMsScan scandata = e.GetScan();
if (runTimeKeeper.Elapsed > intendedRunTime)
{
Console.WriteLine("Ignoring extraneous scan.");
logfile.WriteLine("Ignoring extraneous scan.");
}
else
{
Console.Write('<');
planner_MUT.WaitOne();
Console.Write('_');
runProgram.receiveScan(scandata);
scandata.Dispose();
planner_MUT.ReleaseMutex();
Console.Write('>');
logfile.Flush();
}
}
catch (Exception err)
{
Console.WriteLine("Caught error in scanArrived_response! Cancelling voltage.");
change_voltage(0);
Console.WriteLine(err.ToString());
throw;
}
}
public override void receiveScan(IMsScan scanData)
{
//IInfoContainer info = scanData.CommonInformation;
//IInfoContainer more_info = scanData.SpecificInformation;
//MsScanInformationSource infosource = MsScanInformationSource.Unknown;
object obj_holder = null;
ScanType scan_id = ScanType.Unknown;
int scannum = -1;
//if (info.TryGetRawValue("Scan", out obj_holder, ref infosource))
//{
// scannum = (int)obj_holder;
// if (ScanID.ContainsKey(scannum)) // Auto-scans also have Scan numbers!
// {
// scan_id = ScanID[scannum];
// ScanID.Remove(scannum);
// }
//}
//object accessid = null;
if (scanData.SpecificInformation.TryGetRawValue("Access Id:", out obj_holder))
{
scannum = (int)obj_holder;
if (ScanID.ContainsKey(scannum))
{
scan_id = ScanID[scannum];
ScanID.Remove(scannum);
}
}
//Debug.Assert(false);
if (scannum >= ScanCount)
{
Console.WriteLine("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
log_write("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
ScanCount = scannum + 1;
}
//else if (scannum + 100 < ScanCount)
//{
// Console.WriteLine("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// log_write("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// ScanCount = scannum + 1;
//}
Console.WriteLine("Received a " + scan_id.ToString() + " " + scannum.ToString());
log_write("Received a " + scan_id.ToString() + " " + scannum.ToString());
switch (scan_id)
{
case ScanType.MS2:
case ScanType.Auto:
case ScanType.Unknown:
return;
case ScanType.MS1:
MS1_outstanding = false;
IEnumerable <Tuple <double, double> > scan = Spectral_Processing.ConvertCentroids(scanData.Centroids);
List <Tuple <int, Tuple <double, double> > > molecular_peaks = Spectral_Processing.deisotope_scan(scan);
IEnumerable <Tuple <int, Tuple <double, double> > > valid_precursors = molecular_peaks.Where(x => x.Item1 > 1);
IEnumerable <Tuple <int, Tuple <double, double> > > precursors_by_int = valid_precursors.OrderByDescending(OrderPeak);
GenerateMS2s(precursors_by_int);
Console.WriteLine("MS1 stats: " + scan.Count() + " " + valid_precursors.Count());
log_write("MS1 stats: " + scan.Count() + " " + valid_precursors.Count());
return;
default:
Debug.Assert(false);
return;
}
}
public MSScanEventArgs(SimScan simScan)
{
scan = simScan;
}
public override void receiveScan(IMsScan scanData)
{
//IInfoContainer info = scanData.CommonInformation;
//IInfoContainer more_info = scanData.SpecificInformation;
//MsScanInformationSource infosource = MsScanInformationSource.Unknown;
object obj_holder = null;
ScanType scan_id = ScanType.Unknown;
int scannum = -1;
//if (info.TryGetRawValue("Scan", out obj_holder, ref infosource))
//{
// scannum = (int)obj_holder;
// if (ScanID.ContainsKey(scannum)) // Auto-scans also have Scan numbers!
// {
// scan_id = ScanID[scannum];
// ScanID.Remove(scannum);
// }
//}
//object accessid = null;
if (scanData.SpecificInformation.TryGetRawValue("Access Id:", out obj_holder))
{
scannum = (int)obj_holder;
if (ScanID.ContainsKey(scannum))
{
scan_id = ScanID[scannum];
ScanID.Remove(scannum);
}
}
if (scannum > ScanCount)
{
Console.WriteLine("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
log_write("Adjusting ScanCount: " + scannum.ToString() + " " + ScanCount.ToString());
ScanCount = scannum + 1;
}
//else if (scannum + 100 < ScanCount)
//{
// Console.WriteLine("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// log_write("Adjusting ScanCount DOWNWARD: " + scannum.ToString() + " " + ScanCount.ToString());
// ScanCount = scannum + 1;
//}
Console.WriteLine("Received a " + scan_id.ToString() + " " + scannum.ToString());
log_write("Received a " + scan_id.ToString() + " " + scannum.ToString());
switch (scan_id)
{
case ScanType.MS1:
case ScanType.MS2:
case ScanType.Auto:
case ScanType.Unknown:
// Only Box-MS1 scans are being used for precursor assignment.
// Other scans are merely written to the file automatically.
return;
case ScanType.BoxMS1_1:
case ScanType.BoxMS1_2:
case ScanType.BoxMS1_3:
//MS1_outstanding -= 1;
Debug.Assert(!BoxAggregation.ContainsKey(scan_id));
BoxAggregation.Add(scan_id, Spectral_Processing.ConvertCentroids(scanData.Centroids).ToList());
Console.WriteLine("Received MS1 " + MS1_outstanding.ToString() + " " + BoxAggregation.Count().ToString());
if (BoxAggregation.Count() >= 3)
{
log_write("Processing boxes. " + BoxAggregation.Keys.ToString());
MS1_outstanding = false;
IEnumerable <Peak> scan = BoxesToMS1();
List <Peak> molecular_peaks = Spectral_Processing.deisotope_scan(scan);
IEnumerable <Peak> valid_precursors = molecular_peaks.Where(x => x.Item1 > 1);
IEnumerable <Peak> precursors_by_int = valid_precursors.OrderByDescending(OrderPeak);
GenerateMS2s(precursors_by_int);
}
return;
default:
Debug.Assert(false);
return;
}
}
public abstract void receiveScan(IMsScan scanData);